We just covered this in a recent thread.
Any clear coat applied over a flat paint will make the color appear darker. Applying a flat coat over a clear gloss will not lighten the color to match the adjacent area. This is because the coating is deeper where both the gloss and flat are present, resulting in more internal reflection and refraction in that area.
To avoid this, gloss coat the entire surface, apply decals, then apply a full coverage clear flat.
An interesting technique is to gloss coat only the panels where the decals occur, which serves to differentially weather the panels.